This is a best-practice sort of a question.
We have to deal with segmenting thin bones in large volumes (e.g., 1024^3 or even larger) quite often. The typical suggestion on the forum has been to oversample the segmentation (eg., Segmenting narrow bone structures).
I am doing some tests on how to do this effectively, and the pattern emerging to me is that it is actually more memory effective to oversample the master volume prior to segmentation. Here is what I did:
I loaded MRHEAD.nrrd and used the cropvolume with isotropic voxel setting and 0.25 scaling. I fed the resultant cropped volume to segmentation, and did a threshold range of 97-max. Reported memory usage for this flow was 4800MB on windows.
In a new session, I loaded MRhead, and processed directly with threshold. Then I edited the segmentation geometry such that oversampling was 4, and isotropic voxel is selected. This took 2-3 times longer to process resampling, and in the end reported memory usage on windows was 20264MB.
I am a bit surprised with the result, as I thought the latter would be more memory efficient way of doing things… This is on windows, with 4.11.0-2020-06-16 r29150 / ce703c1